Il est indispensable pour comprendre la diagenèse, i.e., la formation des roches sédimentaires, le durcissement des matériaux de construction hydrauliques comme le ciment ou le plâtre, ou la biominéralisation, d'identifier les mécanismes élémentaires de la cristallisation minérale. Le taux de réaction macroscopique des minéraux est généralement déduit de mesures de chimie des solutions. A côté de ces mesures macroscopiques, l'étude de la réactivité des minéraux inclut maintenant l'analyse des mécanismes atomiques a l'origine des réactions chimiques. Cela a été rendu possible depuis deux décennies par l'apparition d'outils capables d'observer des surfaces avec une résolution nanométrique, tels que la microscopie à force atomique et l'interférométrie à balayage vertical. Le gypse et la calcite font partie des minéraux dits mous. Ce sont des minéraux extrêmement répandus, que l'on peut trouver autant dans la nature sous forme de roches sédimentaires que dans le monde industriel. Le gypse (CaSO4,2H2O) est une évaporite dont les applications incluent la fabrication des plaques de plâtre, l'ajout au ciment Portland comme retardateur, l'élaboration du plâtre de Paris et l'amendement des sols. La sélénite ou l'albâtre sont des variétés de gypse utilisés comme matériaux pour l'ornement, mais leur faible dureté limite leur durabilité. La calcite, forme la plus stable de CaCO3, est un des principaux biominéraux, et un des constituants majeurs des roches des réservoirs carbonates, stockant naturellement de l'eau, du pétrole ou du gaz naturel. Quand les organismes biologiques font croitre leur coquille, ils contrôlent la morphologie, la taille, l'orientation et même la phase des cristaux de carbonates de calcium qui la constituent. Cela conduit à des biomatériaux présentant des propriétés physiques et chimiques qui diffèrent significativement de ceux de la calcite inorganique. Une connaissance plus approfondie des mécanismes sous-jacents à la réactivité de surface de la calcite et de l'effet des impuretés sur celle-ci permettra de nous rapprocher de la possibilité de synthétiser des minéraux biomimétiques, aux propriétés comparables à celles de la calcite biogénique. Dans ce contexte, ma thèse s'est développée dans trois directions. Dans la première, j'ai étudié l'influence d'une contrainte mécanique sur les mécanismes de dissolution. Mon objectif dans cette partie a été de tacher de déduire le taux de dissolution macroscopique à partir de la cinétique des mécanismes atomiques. La seconde partie de la thèse, la plus conséquente, a consisté à étudier l'influence d'une contrainte mécanique sur la croissance de la calcite, et à sonder le rôle d'un additif organique lors de cette croissance sous contrainte. Dans la troisième partie, je me suis penchée sur la dissolution de cristaux de calcite à l'aide de mesures topographiques quantitatives sur des aires relativement étendues de la surface des cristaux, dans une large gamme de pH. J'ai en particulier étudié l'influence d'un additif organique sur la dissolution et la cinétique de réaction à grande échelle. Les taux de dissolution macroscopique et microscopique, c'est-à-dire déduits de la dynamique d'évènements moléculaires (croissance de piqure d'attaque, migration de marche atomique), ne sont presque jamais en accord, même qualitativement, et l'élaboration d'une théorie générale liant la cinétique du phénomène aux deux échelles est encore en cours. Je présente ici des taux de dissolution microscopique du gypse, mesures par microscopie par force atomique (AFM), en accord quantitatif avec les taux de dissolution macroscopiques. Cet accord inédit a été obtenu en prenant soin de neutraliser le biais induit par le fait que la pointe AFM applique une force sur la surface qu'elle sonde, et en identifiant avec soin les mécanismes moléculaires majeurs à l'œuvre lors de la dissolution...[etc] / Identifying reaction mechanisms of minerals is fundamental to understand diagenesis, i.e, sedimentary rock formation, construction material, like cement or gypsum, hardening, and biomineralization. The macroscopic reaction rates of minerals are generally deduced from solution chemistry measurements. Beside the measurement of macroscopic reaction rates, the study of the reactivity of minerals includes now the investigation of the atomic mechanisms involved in the reactions. This has been made possible for two decades by the use of tools resolving nanometric objects, such as vertical scanning interferometry (VSI) and atomic force microscopy (AFM). Gypsum and calcite are among soft minerals. They are extremely widespread mineral that can be found naturally in sedimentary rocks. They are also used in many industrial fields. Gypsum (CaSO4,2H2O) is an evaporate mineral. Gypsum uses include: manufacture of wallboards, plaster of Paris, soil conditioning, and hardening retarder in Portland cement. Varieties of gypsum known as "satin spar" and "alabaster" are used for a variety of ornamental purposes; however, their low hardness limits their durability. Calcite, the most stable crystalline form of CaCO3, is moreover important as a bio-mineral and a major constituent of host rock in carbonate reservoirs, which host drinking water and natural oil and gas. When biological organisms grow their shells, they control the crystal morphology, size, orientation and even the crystal phase of precipitated calcium carbonate. This results in materials with physical and chemical properties that differ significantly from those of inorganically precipitated calcite. Gaining more insight into the surface reactivity of calcite and the effect of surface impurities will bring us one step closer to being able to synthesize biomimetic material, which mimic the properties of biogenic calcite. In this thesis, I had three main focus points. In the first part I studied the effect of stress on the dissolution mechanisms. I investigated to deduce the dissolution rate from the atomic kinetics. The second and the most extensive was the study of the influence of stress on the calcite growth and probing the role of an organic additive on the dynamics of calcite growth while applying stress. In the third part I emphasised on quantitative topographic measurements of dissolving calcite crystal over a relatively large and fixed view at vast range of pH. I considered the influence of an organic additive on the dissolution and surface reaction kinetics at this larger scale. Both macroscopic and microscopic dissolution rates can also be deduced from the dynamics of molecular events (etch pit growth, atomic step migration), but they hardly ever agree, even qualitatively, and the elaboration of a general theory linking the kinetics at the two scales is still in progress. I presented here microscopic dissolution rates of gypsum, measured by atomic force microscopy (AFM), in quantitative agreement with macroscopic rates. This agreement has been obtained in taking care to neutralize the bias induced by the force applied by the AFM tip on the surface, and to identify clearly the driving molecular mechanism. The force applied by the AFM tip on the surface has been seen to increase the solubility of the mineral, thereby introducing a bias, so I have always worked with a constant and low applied force. This result shows that the determination, among the topographic changes during the dissolution of a mineral, of the dominant one, and the measurement of its dynamics, may permit deducing from AFM experiments a reliable macroscopic dissolution rate. The transformation of loose grains into a cohesive solid requires the crystallites to grow eventually constrained by the surrounding grains. Whereas never measured, this confinement and the associated stress is expected to influence noticeably the growth, and the final properties of the material… [etc]

A biomineralização óssea é um processo complexo e multifatorial sendo um grande desafio para a ciência à compreensão dos seus mecanismos regulatórios. Este processo é mediado pela liberação de vesículas da matriz (MVs), as quais surgem das superfícies de osteoblastos e são secretadas no local específico do início da biomineralização. MVs têm a capacidade de acumular altas concentrações de íons Ca2+ e fosfato (Pi), proporcionando um microambiente adequado para a formação inicial e propagação dos cristais de hidroxiapatita. Especial atenção deve ser dada a duas proteínas: Anexina V (AnxA5) e Fosfatase Alcalina (TNAP). As anexinas são as proteínas mais abundantes detectadas nas MVs e responsáveis pela formação de canais de cálcio. TNAP apresenta atividade fosfomonohidrolítica, produzindo Pi a partir, principalmente, de pirofosfato (PPi) e ATP. O enfoque deste projeto foi produzir e caracterizar proteolipossomos com diferentes composições lipídicas de dipalmitoil fosfatidilcolina (DPPC) e dipalmitoil fosfatidilserina (DPPS) contendo TNAP e AnxA5, e manter a funcionalidade das proteínas após incorporação nos sistemas miméticos. Foi possível incorporar AnxA5 em DPPC-proteolipossomos (11,64 µg/mL), mas na presença de DPPS houve um aumento significativo de AnxA5 incorporada (25,79 µg/mL) a DPPC:DPPS 10%-proteolipossomos (razão molar). A presença das proteínas nos proteolipossomos compostos por DPPC e DPPC:DPPS 5, 10 e 15% (razão molar) foi confirmada por SDS-PAGE e Immunoblotting. Melhores rendimentos de incorporação das duas proteínas foram obtidos quando ambas foram incorporadas concomitantemente. DPPC-proteolipossomos e DPPC:DPPS 10%-proteoliposomos revelaram conter 75% de AnxA5 e 25% de TNAP em concentração de proteína. A presença de DPPS não afetou significativamente as porcentagens de proteínas incorporadas. Os parâmetros cinéticos da TNAP na hidrólise de diferentes substratos fisiológicos (ATP, ADP e PPi) foram determinados na presença e ausência de AnxA5, em pH fisiológico, e para os diversos sistemas lipídicos. A melhor eficiência catalítica da enzima foi obtida para sistemas contendo 10% de DPPS (razão molar) (kcat/K0.5= 183,02; 776,06 e 657,08 M-1.s-1, respectivamente). A TNAP apresentou maior especificidade para a hidrólise de PPi quando comparado com ATP e ADP. Estudos utilizando Calorimetria Diferencial de Varredura (DSC) mostraram que o aumento da concentração de DPPS em DPPC-lipossomos proporcionou um progressivo alargamento no pico de transição de fase, diminuição na t1/2 e H. A pré-transição de fase só foi detectada até a concentração de 15% de DPPS em DPPC. Para 20% de DPPS e acima, observou-se uma segregação lateral de fase com a formação de possíveis microdomínios ricos em DPPS. A interação da AnxA5 com DPPC-lipossomos e DPPC:DPPS 10%-lipossomos resultou em uma redução nos valores de H (de 8,73 para 5,68 e 8,43 para 5,37 Kcal.mol-1, respectivamente). Quando a TNAP está presente nos proteolipossomos, este efeito é ainda maior. A AnxA5 incorporada em DPPC-proteolipossomos e DPPC:DPPS 10%-proteolipossomos (razão molar) foi capazes de mediar o influxo de 45Ca2+ para dentro das vesículas (~ 800 nmol Ca2+) quando utilizados faixas de concentração de cálcio em níveis fisiológicos (~2 mM). A presença da TNAP nos proteolipossomos não afetou o influxo de Ca2+ mediado pela AnxA5. Entretanto, a presença da AnxA5 afetou significativamente os parâmetros cinéticos da TNAP para os diferentes substratos. Estudos com vesículas unilamelares gigantes (GUVs) também confirmaram a inserção funcional da AnxA5 em vesículas constituídos de dioleoil fosfatidilcolina (DOPC) e DOPC:DPPS 10% (razão molar). O principal efeito causado pela AnxA5 na morfologia das GUVs foi a perda de contraste óptico devido a formação de poros nas membranas das vesículas. Neste caso, a presença de DPPS não proporcionou mudanças significativas para a incorporação da AnxA5. TNAP quando inserida em GUVs provocou intensa flutuação e excesso de área das vesículas com formação de filamentos. A presença do DPPS provavelmente dificulta a inserção da TNAP à membrana das GUVs. Quando há microdomínios lipídicos heterogêneos na composição de GUVs compostas por DOPC:Colesterol:Esfingomielina (8:1:1) e DOPC:Colesterol:Esfingomielina:Gangliosídeo (7:1:1:1) (razão molar), a inserção da TNAP provocou uma maior segregação lateral de fase evidenciada por imagens com fluorescência. A presença da TNAP e AnxA5 em DPPC:DPPS 10%-proteolipossomos proporcionou mudanças significativas nas propriedades mecânicas visco-elásticas dos proteolipossomos detectadas por imagens de Microscopia de Força Atômica. Assim, no presente trabalho foi possível obter uma inédita metodologia para a formação de proteolipossomos contendo TNAP e AnxA5 concomitantemente, os quais apresentaram uma reconstituição funcional das proteínas, apresentando capacidade de captar Ca2+ para dentro das vesículas e habilidade de hidrolisar fosfosubstratos em sua superfície. / Bone biomineralization is a multifactorial and complex process, being a challenge for the science the understanding of their regulatory mechanisms. This process is mediated by the release of matrix vesicles (MVs), structures which arise by budding from osteoblast and chondroblast surface and are secreted in the specific site where biomineralization begins. MVs have the ability of accumulating high concentrations of Ca2+ and Pi ions, providing an adequate microenvironment for the initial formation and propagation of hydroxyapatite crystals. Two protein families present in MVs merit special attention: Annexins and Phosphatases. The annexins were the most abundant proteins detected in MVs and are responsible for the Ca2+-channels formation (especially AnxA5). Tissue-nonspecific alkaline phosphatase (TNAP) exhibits phosphomonohydrolytic activity, producing Pi mainly from PPi and ATP. Such proteins regulate the formation of calcium phosphate crystals, acting directly in the bone mineralization process. The goal of this project was to produce and characterize proteoliposomes with different lipid compositions of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylserine (DPPS) harboring TNAP and AnxA5, keeping the functions of both proteins after their incorporation into the mimetic systems. AnxA5 was able to incorporate into DPPC-proteoliposomes (11.64 µg/mL), but the presence of DPPS increased significantly the AnxA5 incorporation (25.79 µg/mL) into DPPC:DPPS 10%-proteoliposomes. The presence of both proteins into DPPC and DPPC:DPPS 5, 10 and 15% (molar ratios) proteoliposomes was confirmed by SDS-PAGE and Immunoblotting analysis. Better yield of TNAP and AnxA5 incorporation was observed when both proteins were reconstituted simultaneously. DPPC-proteoliposomes and DPPC:DPPS 10%-proteoliposomes (molar ratio) incorporated about 75% of AnxA5 and 25% of TNAP (protein concentration). DPPS presence did not affect significantly the yield of incorporation of both proteins. The kinetic parameters for the hydrolysis of different physiological substrates (ATP, ADP and PPi) by TNAP were determined in the presence and absence of AnxA5, at physiological pH, for the different systems. The best catalytic efficiencies were achieved with proteoliposomes containing DPPS 10% (molar ratio) (kcat/K0.5= 183.02; 776.06 and 657.08 M-1.s-1 for ATP, ADP and PPi, respectively), condition that also favored PPi hydrolysis by TNAP when compared to ATP and ADP hydrolysis. Studies by Differential Scanning Calorimetry (DSC) showed that the increasing DPPS concentrations in the DPPC-liposomes resulted in a progressive broadening of the phase transition peaks and decreased t1/2 and H values. The pre-transition was detected only in concentrations up to DPPS 15% in DPPC. Phase lateral segregation can be observed for DPPS 20% and above, suggesting the formation of DPPS-rich microdomains. The interaction of AnxA5 with DPPC and DPPC:DPPS 10%-liposomes resulted in a decrease of H values (from 8.73 to 5.68 and from 8.43 to 5.37 Kcal.mol-1, respectively). When TNAP was present in the proteoliposomes, this effect was even greater. AnxA5 incorporated into DPPC and DPPC:DPPS 10%-proteoliposomes (molar ratio) was able to mediate 45Ca2+-influx (~ 800 nmol Ca2+) into the vesicles at physiological Ca2+-concentrations (~ 2 mM), and this process was not affected by the presence of TNAP in the systems. However, AnxA5 affected significantly the hydrolysis of substrates by TNAP. Studies with Giant Unilamellar Vesicles (GUVs) also confirmed the functional reconstitution of AnxA5 in dioleoylphosphocholine (DOPC) and DOPC:DPPS 10% (molar ratio) vesicles. The main effect caused by AnxA5 in the GUVs morphology was the formation of pores in the vesicles membrane. In this case, DPPS presence did not affect the AnxA5 incorporation. The presence of TNAP in GUVs caused a several fluctuation, indicating that the vesicles acquired an excess of area and undergoes sequential budding transitions. It is suggested that the presence of DPPS makes the TNAP insertion into the GUVs membrane difficult. With the presence of heterogeneous lipid microdomains in GUVs composed of DOPC, Cholesterol (Chol), Sphingomyelin (SM) and Ganglioside (GM1) in the proportions DOPC:Chol:SM 8:1:1 and DOPC:Chol:SM:GM1 7:1:1:1 (molar ratios), the TNAP insertion caused a greater phase lateral segregation, evidenced by fluorescence analysis. Atomic Force Microscopy (AFM) analysis indicated that the presence of both proteins into DPPC:DPPS 10%-proteoliposomes (molar ratio) caused significant changes in the visco-elastic mechanical properties of the vesicles. In conclusion, the present work describes the synthesis of proteoliposomes harboring TNAP and AnxA5 concomitantly, with the functional reconstitution of both proteins, with the ability to transport Ca2+ into the vesicles and hydrolyze phosphosubstrates on their surface.

In dieser Arbeit ist es gelungen, die Bedeutung physikalisch-chemischer Mechanismen in der Biomineralisation gegenüber der bisher angenommenen Dominanz spezifischer biomolekularer Erkennungsmechanismen aufzuzeigen. Dazu wurden drei Ansätze verfolgt: Zum einen wurden Studien zur Calciumcarbonatkristallisation durchgeführt. Zum anderen wurde das Biomineral Perlmutt intensiv untersucht. Als drittes wurde ein Modellsystem entwickelt, mit dem künstliches Perlmutt synthetisiert und ein Mechanismus für die Perlmuttmineralisation vorgeschlagen werden konnte. <br><br> Im ersten Schritt wurden in einem simplen Kristallisationsansatz komplexe Calciumcarbonatüberstrukturen ohne die Verwendung von Additiven synthetisiert. Es wurde gezeigt, daß diese durch orientierte Anlagerung von Nanopartikeln gebildet werden, bei der dipolare Felder eine wichtige Rolle zu spielen scheinen. Dieser Mechansimus war bislang für Calciumcarbonat unbekannt und ermöglicht die Synthese komplexer Kristallmorphologien, wodurch die Frage aufgeworfen wird, ob er bei der Biomineralbildung von Bedeutung sein kann. Durch Einsatz minimaler Mengen eines einfachen, synthetischen Additivs bei der Kristallisation wurden zu Überstrukturen angeordnete Aragonitplättchen synthetisiert, die von einer wenige nm dicken Schicht aus amorphen Calciumcarbonat umgeben sind. Eine solche Schicht wurde auch bei den Aragonitplättchen Perlmutts entdeckt (s.u.) und bietet möglicherweise in verschiedenen Systemen eine Erklärung für die Stabilisierung der sonst metastabilen Aragonitphase. <br><br> Im zweiten Schritt wurden bei der Untersuchung von natürlichem Perlmutt zwei bislang unbekannte Strukturmerkmale entdeckt: Es gibt Bereiche, die nicht aus den charakteristischen Plättchen bestehen, sondern wesentlich weniger stark mineralisert sind. Die Mineralphase besteht in diesen Bereichen aus Nanopartikeln. Es wurde weiterhin gezeigt, daß die Aragonitplättchen von einer wenige nm dicken Schicht aus amorphem Calciumcarbonat umgeben ist. Die gängigen Modelle der Perlmuttbildung sind mit diesen Beobachtungen nicht zu vereinbaren und somit zu hinterfragen. Dagegen deuten diese Ergebnisse ein Wachstum von Perlmutt über ACC-Nanopartikel an. <br><br> Unter der Annahme der Bedeutung physikalisch-chemischer Mechanismen in der Biomineralisation wurde schließlich als dritter Schritt ein Ansatz zur in vitro-Retrosynthese von Biomineralien ausgehend von ihrer unlöslichen Matrix entwickelt. <br><br> Mit diesem Ansatz ist es erstmals gelungen, künstliches Perlmutt auf synthetischem Wege herzustellen, das morphologisch nicht vom Original zu unterscheiden ist. Die existierenden Unterschiede konnten zeigen, daß der Mineralisationsprozeß nicht auf ein spezifisches Mikroumgebungssystem beschränkt, sondern "allgemeiner gültig"' sein muß. <br><br> Bei der Retrosynthese gibt es zwei Schlüsselfaktoren: Zum einen die demineralisierte unlösliche Perlmuttmatrix als dreidimensionales Gerüst für das künstliche Perlmutt, zum anderen amorphe Precursorpartikel, die die Mineralphase bilden. Es werden keinerlei Proteine oder andere Biomoleküle verwendet. Dieser Ansatz bietet die Möglichkeit, den Mineralisationsprozeß an einem in vitro-Modellsystem zu verfolgen, was für das in vivo-System, wenn überhaupt, nur unter starken Einschränkungen möglich ist.<br><br> Es wurde gezeigt, daß das künstliche Perlmutt über die Mesoskalentransformation von ACC-Precursorn innerhalb der Matrix gebildet wird und als möglicher Mechanismus bei der Biomineralisation von natürlichem Perlmutt diskutiert. Es konnte in der vorliegenden Arbeit konsequent gezeigt werden, daß die Imitation von Biomineralisationsprozessen in in vitro-Ansätzen möglich ist, wobei chemisch-physikalische Parameter dominieren. <br><br> In zukünftigen Studien sollten einerseits die mechanischen Eigenschaften des künstlichen Perlmutts untersucht werden, wofür sich in Vorversuchen im Rahmen dieser Arbeit die Nanoindentierung als geeignet herausgestellt hat. Es sollte geprüft werden, ob das hier ermittelte Prinzip zur Mineralisierung in der Materialentwicklung angewendet werden kann. Andererseits sollte die Retrosynthese auf andere Systeme ausgeweitet und in vivo-Studien durchgeführt werden, um die Gültigkeit der vorgeschlagenen Mechanismen zu überprüfen. / This thesis highlights the importance of physical-chemical mechanisms in biomineralisation and, thus, challenges the widely accepted dominance of specific biomolecular recognition mechanisms. <br><br> The work is divided into three parts: the first part addresses the crystallisation of calcium carbonate; the second part focuses on an intensive study of the biomineral, nacre, and, lastly, a retrosynthesis model system is designed and applied to synthesize artificial nacre. A mechanism for nacre mineralisation in nature is proposed. <br><br> Initially, complex calcium carbonate superstructures were synthesized in the absence of any additive. These were shown to grow by an oriented attachment mechanism of nanoparticles, presumably under the influence of dipolar fields. This growth mechanism has, to date, not been described for calcium carbonate. This mechanism opens the possibility to synthesize complex crystal morphologies of calcium carbonate and arises the question as to whether it plays a role in the growth of biominerals. <br><br> With the presence of small amounts of additives in calcium carbonate crystallisation it was possible to synthesize superstructures of aragonite platelets, each of which surrounded by a layer of amorphous calcium carbonate (ACC). Such ACC layers were also found in natural nacre (see below) and may explain the stabilisation of the metastable calcium carbonate polymorph aragonite. <br><br> In the second part of this thesis two unknown features of nacre structures were distinguished: Some areas within the nacre do not consist of the characteristic aragonite platelets but are mineralized only to a low degree. In these areas the mineral phase is clearly composed of nanoparticles. Furthermore, the aragonite platelets of nacre are shown to be surrounded by an ACC layer. Both observations contradict the classical models of nacre growth mechanisms but hint towards a growth via ACC nanoparticles. <br><br> Assuming the importance of physical-chemical mechanisms in biomineralisation, an approach for the in vitro retrosynthesis of biominerals was designed. Through this, it was possible, for the first time, to synthesize artificial nacre, which was indistinguishable in morphology from the original. The non-morphological differences between original and synthesized nacre showed that the biological process of mineralization is not limited to one specific microenvironment, but must be more general. <br><br> Two key factors are of importance for the retrosynthesis approach: 1) The demineralised nacre matrix, which forms a scaffold for the artificial mineral phase and; 2) amorphous nanoparticles as precursors, which transform into the mineral phase. No proteins or other biomolecules were utilized. In this way, the biomineralisation process could be followed in an in vitro model, a process, which is hardly possible in such detail under in vivo conditions. This work proves that the artificial nacre grows by a mesoscale transformation of ACC nanoparticles, and discusses this mechanism as a possible growth mechanism of natural nacre. This work consequently shows that it is possible to imitate biomineralisation processes in vitro and that, in–vitro, these processes are driven by physico-chemical parameters. <br><br> Future studies will involve investigation of the mechanical properties of the artificial nacre. First experiments indicate, that nanoindentation is hereby suitable. The potential application of the in vitro mineralization mechanism for new material development will be investigated. Furthermore, the retrosynthesis will be applied to other biomineral systems and, subsequently, in vivo studies will be performed so as to investigate the role of the proposed mechanisms for the natural biomineralisation process.

This study is focused on the fabrication of plasma polymerized ultrathin films and the elucidation of their unique properties with an emphasis on the solvent-less, dry polymerization process to introduce post-deposition functionality, robustness, and shape preservation. Two major classes of materials are the subject of this study: biological monomers, specifically the amino acids tyrosine and histidine and synthetic organic and inorganic monomers including acrylonitrile, 2-hydroxyethyl methacrylate, N-isopropylacrylamide, titanium isopropoxide and ferrocene. The unique chemical and physical properties of highly cross-linked ultrathin plasma polymerized amino acid and synthetic polymer films are demonstrated along with their functional response and robustness on both planar and complex surface structures. The work emphasizes the facile ability of plasma polymerization to create unique, tailored ultrathin coatings. Chemical functionality retention (OH, NH₂) of the tyrosine and histidine amino acids is demonstrated by the subsequent mineralization of gold or titania nanoparticles on the plasma polymerized ultrathin films using a wet chemical approach. Inorganic nanoparticle mineralization is further investigated as a method to modify the optical properties of composite nanocoatings. Plasma co-polymerization of tyrosine and synthetic monomers is used to create nanocomposite coatings with unique surface functionalities, responsive behavior, optical characteristics and a high level of integration between monomers. The fabrication of novel plasma polymerized Janus microspheres, micropatterned substrates and free-standing films also demonstrate numerous plasma polymerized materials which exhibit unique structural properties. Overall, facile plasma polymerization of novel, functional ultrathin films and complex topological coatings having potential biocompatible and optical applications is established.

Die Schwingungsspektroskopie, besonders die Raman-Spektroskopie, stellt ein wichtiges Werkzeug für Untersuchungen von Biomineralien dar. Raman-Spektroskopie wurde zur Untersuchung der organischen und anorganischen Bestandteile von Schwammskeletten eingesetzt. Die Raman-Spektroskopie trug auch zur Charakterisierung von biomimetischen Silikat-Präzipitaten bei. Durch ortsaufgelöste Raman-Spektroskopie konnte erstmalig die Verteilung von organischem Material in den extrahierten Silikatzellwänden von Kieselalgen nachgewiesen werden. Die ortsaufgelöste Raman-Spektroskopie wurde ebenfalls zur Untersuchung des SERS-Effekts an Zellwänden von Kieselalgen an die Silber-Nanopartikel gekoppelt waren eingesetzt.

Les bactéries magnétotactiques représentent un groupe d’une grande diversité écologique et phylogénétique. Elles sont capables de biominéraliser des nanocristaux de magnétite [un oxyde de fer (Fe(II)Fe(III)2O4)] ou de greigite [un sulfure de fer (Fe(II)Fe(III)2S4)] dans leurs magnétosomes, organites alignés en chaînes permettant la navigation le long des lignes de champ magnétique terrestre. Jusqu'à récemment, seules des souches produisant de la magnétite étaient disponibles en culture pure, conduisant à des études sur les mécanismes de biominéralisation de cet oxyde de fer. En 2011, une nouvelle bactérie capable de former de la magnétite et de la greigite, Desulfamplus magnetovallimortis souche BW-1, a été cultivée avec succès en laboratoire. Dans cette thèse, nous proposons d'utiliser une approche intégrée et multidisciplinaire pour comprendre les mécanismes de biominéralisation de la greigite en utilisant comme modèle d’étude la souche BW-1. Nous avons donc cherché à déterminer les conditions environnementales et biologiques favorisant la formation de la magnétite et de la greigite. Ces travaux ont également conduit à la caractérisation physiologique et phylogénétique de BW-1. Puis, l’utilisation d’approches globales et ciblées de transcriptomique ont permis d'évaluer le taux d'expression des gènes impliqués dans la formation des magnétosomes (magnétite vs. greigite) dans diverses conditions de croissance. Une approche de protéomique a permis d’apporter des informations supplémentaires à cette étude. Ces résultats ont permis de progresser dans la compréhension fondamentale de la biominéralisation in vivo, en particulier pour des bactéries formant de la greigite. / Magnetotactic bacteria represent a phylogenetically and ecologically diverse group of prokaryotes able to biomineralize magnetic nanocrystals composed of magnetite [an iron oxide (Fe(II)Fe(III)2O4)] or greigite [an iron sulfide (Fe(II)Fe(III)2S4)] in their magnetosomes, a prokaryotic organelle whose cytoplasmic alignement in chain allows the cell to navigate along the Earth’s magnetic field lines. Until recently, only magnetite-producing strains were available in pure culture. Thus, only the magnetite biomineralization has been studied. In 2011, a new bacterium able to form both magnetite and greigite, Desulfamplus magnetovallimortis strain BW-1, was isolated from Death Valley, California and cultivated in pure culture. In this work, we propose to use an integrated and multidisciplinary approach to understand the mechanisms involved in greigite biomineralization in BW-1 strain. First, we determined the environmental and biological conditions in which magnetite and greigite are formed. This first part of my thesis also contributed to the physiologic and phylogenetic characterization of this bacterium. Secondly, we used global and targeted transcriptomic approaches to evaluate the transcription levels of genes putatively involved in magnetosomes formation (magnetite vs. greigite) under various growth conditions. A proteomic approach provided additional informations to this study.Results obtained during my thesis contribute to the understanding of in vivo biomineralization, particularly for greigite production in magnetotactic bacteria.

A biomineralização óssea é um processo complexo e multifatorial sendo um grande desafio para a ciência à compreensão dos seus mecanismos regulatórios. Este processo é mediado pela liberação de vesículas da matriz (MVs), as quais surgem das superfícies de osteoblastos e são secretadas no local específico do início da biomineralização. MVs têm a capacidade de acumular altas concentrações de íons Ca2+ e fosfato (Pi), proporcionando um microambiente adequado para a formação inicial e propagação dos cristais de hidroxiapatita. Especial atenção deve ser dada a duas proteínas: Anexina V (AnxA5) e Fosfatase Alcalina (TNAP). As anexinas são as proteínas mais abundantes detectadas nas MVs e responsáveis pela formação de canais de cálcio. TNAP apresenta atividade fosfomonohidrolítica, produzindo Pi a partir, principalmente, de pirofosfato (PPi) e ATP. O enfoque deste projeto foi produzir e caracterizar proteolipossomos com diferentes composições lipídicas de dipalmitoil fosfatidilcolina (DPPC) e dipalmitoil fosfatidilserina (DPPS) contendo TNAP e AnxA5, e manter a funcionalidade das proteínas após incorporação nos sistemas miméticos. Foi possível incorporar AnxA5 em DPPC-proteolipossomos (11,64 µg/mL), mas na presença de DPPS houve um aumento significativo de AnxA5 incorporada (25,79 µg/mL) a DPPC:DPPS 10%-proteolipossomos (razão molar). A presença das proteínas nos proteolipossomos compostos por DPPC e DPPC:DPPS 5, 10 e 15% (razão molar) foi confirmada por SDS-PAGE e Immunoblotting. Melhores rendimentos de incorporação das duas proteínas foram obtidos quando ambas foram incorporadas concomitantemente. DPPC-proteolipossomos e DPPC:DPPS 10%-proteoliposomos revelaram conter 75% de AnxA5 e 25% de TNAP em concentração de proteína. A presença de DPPS não afetou significativamente as porcentagens de proteínas incorporadas. Os parâmetros cinéticos da TNAP na hidrólise de diferentes substratos fisiológicos (ATP, ADP e PPi) foram determinados na presença e ausência de AnxA5, em pH fisiológico, e para os diversos sistemas lipídicos. A melhor eficiência catalítica da enzima foi obtida para sistemas contendo 10% de DPPS (razão molar) (kcat/K0.5= 183,02; 776,06 e 657,08 M-1.s-1, respectivamente). A TNAP apresentou maior especificidade para a hidrólise de PPi quando comparado com ATP e ADP. Estudos utilizando Calorimetria Diferencial de Varredura (DSC) mostraram que o aumento da concentração de DPPS em DPPC-lipossomos proporcionou um progressivo alargamento no pico de transição de fase, diminuição na t1/2 e H. A pré-transição de fase só foi detectada até a concentração de 15% de DPPS em DPPC. Para 20% de DPPS e acima, observou-se uma segregação lateral de fase com a formação de possíveis microdomínios ricos em DPPS. A interação da AnxA5 com DPPC-lipossomos e DPPC:DPPS 10%-lipossomos resultou em uma redução nos valores de H (de 8,73 para 5,68 e 8,43 para 5,37 Kcal.mol-1, respectivamente). Quando a TNAP está presente nos proteolipossomos, este efeito é ainda maior. A AnxA5 incorporada em DPPC-proteolipossomos e DPPC:DPPS 10%-proteolipossomos (razão molar) foi capazes de mediar o influxo de 45Ca2+ para dentro das vesículas (~ 800 nmol Ca2+) quando utilizados faixas de concentração de cálcio em níveis fisiológicos (~2 mM). A presença da TNAP nos proteolipossomos não afetou o influxo de Ca2+ mediado pela AnxA5. Entretanto, a presença da AnxA5 afetou significativamente os parâmetros cinéticos da TNAP para os diferentes substratos. Estudos com vesículas unilamelares gigantes (GUVs) também confirmaram a inserção funcional da AnxA5 em vesículas constituídos de dioleoil fosfatidilcolina (DOPC) e DOPC:DPPS 10% (razão molar). O principal efeito causado pela AnxA5 na morfologia das GUVs foi a perda de contraste óptico devido a formação de poros nas membranas das vesículas. Neste caso, a presença de DPPS não proporcionou mudanças significativas para a incorporação da AnxA5. TNAP quando inserida em GUVs provocou intensa flutuação e excesso de área das vesículas com formação de filamentos. A presença do DPPS provavelmente dificulta a inserção da TNAP à membrana das GUVs. Quando há microdomínios lipídicos heterogêneos na composição de GUVs compostas por DOPC:Colesterol:Esfingomielina (8:1:1) e DOPC:Colesterol:Esfingomielina:Gangliosídeo (7:1:1:1) (razão molar), a inserção da TNAP provocou uma maior segregação lateral de fase evidenciada por imagens com fluorescência. A presença da TNAP e AnxA5 em DPPC:DPPS 10%-proteolipossomos proporcionou mudanças significativas nas propriedades mecânicas visco-elásticas dos proteolipossomos detectadas por imagens de Microscopia de Força Atômica. Assim, no presente trabalho foi possível obter uma inédita metodologia para a formação de proteolipossomos contendo TNAP e AnxA5 concomitantemente, os quais apresentaram uma reconstituição funcional das proteínas, apresentando capacidade de captar Ca2+ para dentro das vesículas e habilidade de hidrolisar fosfosubstratos em sua superfície. / Bone biomineralization is a multifactorial and complex process, being a challenge for the science the understanding of their regulatory mechanisms. This process is mediated by the release of matrix vesicles (MVs), structures which arise by budding from osteoblast and chondroblast surface and are secreted in the specific site where biomineralization begins. MVs have the ability of accumulating high concentrations of Ca2+ and Pi ions, providing an adequate microenvironment for the initial formation and propagation of hydroxyapatite crystals. Two protein families present in MVs merit special attention: Annexins and Phosphatases. The annexins were the most abundant proteins detected in MVs and are responsible for the Ca2+-channels formation (especially AnxA5). Tissue-nonspecific alkaline phosphatase (TNAP) exhibits phosphomonohydrolytic activity, producing Pi mainly from PPi and ATP. Such proteins regulate the formation of calcium phosphate crystals, acting directly in the bone mineralization process. The goal of this project was to produce and characterize proteoliposomes with different lipid compositions of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylserine (DPPS) harboring TNAP and AnxA5, keeping the functions of both proteins after their incorporation into the mimetic systems. AnxA5 was able to incorporate into DPPC-proteoliposomes (11.64 µg/mL), but the presence of DPPS increased significantly the AnxA5 incorporation (25.79 µg/mL) into DPPC:DPPS 10%-proteoliposomes. The presence of both proteins into DPPC and DPPC:DPPS 5, 10 and 15% (molar ratios) proteoliposomes was confirmed by SDS-PAGE and Immunoblotting analysis. Better yield of TNAP and AnxA5 incorporation was observed when both proteins were reconstituted simultaneously. DPPC-proteoliposomes and DPPC:DPPS 10%-proteoliposomes (molar ratio) incorporated about 75% of AnxA5 and 25% of TNAP (protein concentration). DPPS presence did not affect significantly the yield of incorporation of both proteins. The kinetic parameters for the hydrolysis of different physiological substrates (ATP, ADP and PPi) by TNAP were determined in the presence and absence of AnxA5, at physiological pH, for the different systems. The best catalytic efficiencies were achieved with proteoliposomes containing DPPS 10% (molar ratio) (kcat/K0.5= 183.02; 776.06 and 657.08 M-1.s-1 for ATP, ADP and PPi, respectively), condition that also favored PPi hydrolysis by TNAP when compared to ATP and ADP hydrolysis. Studies by Differential Scanning Calorimetry (DSC) showed that the increasing DPPS concentrations in the DPPC-liposomes resulted in a progressive broadening of the phase transition peaks and decreased t1/2 and H values. The pre-transition was detected only in concentrations up to DPPS 15% in DPPC. Phase lateral segregation can be observed for DPPS 20% and above, suggesting the formation of DPPS-rich microdomains. The interaction of AnxA5 with DPPC and DPPC:DPPS 10%-liposomes resulted in a decrease of H values (from 8.73 to 5.68 and from 8.43 to 5.37 Kcal.mol-1, respectively). When TNAP was present in the proteoliposomes, this effect was even greater. AnxA5 incorporated into DPPC and DPPC:DPPS 10%-proteoliposomes (molar ratio) was able to mediate 45Ca2+-influx (~ 800 nmol Ca2+) into the vesicles at physiological Ca2+-concentrations (~ 2 mM), and this process was not affected by the presence of TNAP in the systems. However, AnxA5 affected significantly the hydrolysis of substrates by TNAP. Studies with Giant Unilamellar Vesicles (GUVs) also confirmed the functional reconstitution of AnxA5 in dioleoylphosphocholine (DOPC) and DOPC:DPPS 10% (molar ratio) vesicles. The main effect caused by AnxA5 in the GUVs morphology was the formation of pores in the vesicles membrane. In this case, DPPS presence did not affect the AnxA5 incorporation. The presence of TNAP in GUVs caused a several fluctuation, indicating that the vesicles acquired an excess of area and undergoes sequential budding transitions. It is suggested that the presence of DPPS makes the TNAP insertion into the GUVs membrane difficult. With the presence of heterogeneous lipid microdomains in GUVs composed of DOPC, Cholesterol (Chol), Sphingomyelin (SM) and Ganglioside (GM1) in the proportions DOPC:Chol:SM 8:1:1 and DOPC:Chol:SM:GM1 7:1:1:1 (molar ratios), the TNAP insertion caused a greater phase lateral segregation, evidenced by fluorescence analysis. Atomic Force Microscopy (AFM) analysis indicated that the presence of both proteins into DPPC:DPPS 10%-proteoliposomes (molar ratio) caused significant changes in the visco-elastic mechanical properties of the vesicles. In conclusion, the present work describes the synthesis of proteoliposomes harboring TNAP and AnxA5 concomitantly, with the functional reconstitution of both proteins, with the ability to transport Ca2+ into the vesicles and hydrolyze phosphosubstrates on their surface.

No description available.

Biologically controlled mineralization implies that organisms devote a part of their physiological activity to build up a specific mineralized skeleton. A preliminary comprehensive general view of the morphology and physiology of a given organism is therefore required before trying to understand where and how its biomineralizing system functions. Furthermore, the entire biomineralization sequence is not mediated by purely inorganic mineralogical rules but rather by a cellular machinery. Accordingly, a mineralogical characterization should be linked to a histological and cytological investigation of mineralizing cells to understand how a skeleton is produced. In the present thesis, we developed such a multi-disciplinary approach of some biomineralization processes of the massive basal skeleton in a few Recent hypercalcified sponges, likely survivors from Palaeozoic and early Mesozoic seas.<p>The three first chapters of this thesis are dedicated to the Mediterranean Calcarea Petrobiona massiliana, a conveniently accessible living hypercalcified sponge whereas all other Recent hypercalcified species are tropical and less easily reached. This model species permitted an initial morphological approach followed by an integrated biological and mineralogical study of biomineralization mechanisms. The fourth chapter aims at the comparative mineralogical study of the basal skeleton of eight tropical Recent hypercalcified demonsponges.<p>In the first chapter, important modifications and/or morphogenesis at the tissular or cellular level in response to life cycle phases and environmental conditions were depicted in specimens of Petrobiona massiliana. A survey of “storage cells” filling trabecular tracts, which are specific to P. massiliana, suggested that these cells may provide energy and a pool of toti- or pluripotent cells able to restructure the aquiferous system and repopulate cell types like pinacocytes. This potentiality of "storage cells would allow the sponge to sustain important physiological activities, like calcification, along its life cycle. Furthermore, basopinacocytes, cells delineating basally the soft tissue from the underlying basal skeleton, were identified through ultrastructural observations as the most probable cell type involved in the formation of the basal skeleton.<p>In the second chapter, the skeleton was found to be composed of ca. 50 to 100 nm crystallized grains as the smallest skeletal units, likely initially deposited in a mushy amorphous state. TEM and SEM observations further highlighted that these submicronic grains were assembled in clusters or fibres, the later even laterally associated into bundles. A model of crystallization propagation through amorphous submicronic granular units is proposed to explain the single-crystal feature of these micron-scale structural units, as demonstrated by selected area electron diffraction (SAED) in TEM. Finally, these units were assembled into a defined microstructure forming flattened growth layers called "sclerodermites", which superposed to produce the massive basal skeleton. In addition, X-ray diffraction (XRD) and energy electron loss spectroscopy (EELS) analyses highlighted respectively heterogeneous concentration and spatial distribution of Mg and Ca ions in the skeleton and structural units. This characterization highlighted mineralogical features, not conforming to the inorganic principles, and presuming a highly biologically regulated construction of the basal skeleton.<p>Accordingly, in the third chapter, it arose that the endomembrane system of basopinacocytes might play a dual function in the production and transport of both mineralizing ions and organic matrices. Combining partial decalcification methods with histochemical dyes and observing ultra-thin sections of the mature basal skeleton in TEM, very spatially and functionally diverse organic matrix components were found to occur in growing and mature portions of the skeleton. The following model of biomineralization was proposed for Petrobiona massiliana: basopinacocytes would use the endomembrane system pathway to produce and carry organic-coated submicronic amorphous grains in a mushy state within intracellular vesicles. These would then be released through the basal cell membrane toward the growing layer of the skeleton, where a highly structured gel-like organic framework, rich in sulfated/acidic GAGs-rich macromolecules, secreted by basopinacocytes, would ensure their assemblage into oriented fibres or clusters.<p>In the fourth chapter, the basal skeleton of eight tropical Recent hypercalcified species belonging to demosponges: Acanthochaetetes wellsi, Willardia caicosensis, Astrosclera willeyana, Ceratoporella nicholsoni, Goreauiella auriculata, Hispidopetra miniana, Stromatospongia norae and Calcifibrospongia actinostromarioides, were compared. Some mineralogical nano- to submicronic patterns already observed in the Calcarea P. massiliana, appeared as general features: the occurrence of submicronic granular units, their coherent assemblage into monocrystalline fibres and bundles and the likely presence of organic material around all structural units. Additional features brought new insights in our comprehension of biomineralization mechanisms in hypercalcified sponges. Among them, micro-twin and stacking-fault planes aligned with the fibres/bundles axis and crossing over submicronic granular units characterized the skeleton of most aragonitic species. This highly supports the crystallization propagation model proposed for P. massiliana, although it additionally suggests that it should occur only after the oriented assemblage of submicronic grains. Furthermore, lighter transverse striations separated by few nanometres occurred systematically in fibres and bundles of the eight basal skeletons investigated, suggesting the involvement of nanoscale intracrystalline fibrils in the biological control.<p>In conclusion, this comparative study of nine Recent hypercalcified sponges belonging to phylogenetically distant taxa resulted in the proposition of a shared biomineralization model based on the production of micron and submicron-scale structural units to build up macro-scale basal skeletons under a high biological control. We suggest that the cellular toolkit used for the biologically controlled biomineralization in these sponges is very ancient<p>and was already developed by their early Palaeozoic ancestors. Furthermore, this model supports recent concepts of calcium carbonate biomineralization developed for example in corals, molluscs and echinoderms, suggesting an even more universal and ancestral character of initial biomineralization mechanisms in all Metazoa producing a calcium carbonate skeleton.<p><p>La minéralisation biologiquement contrôlée implique qu’un organisme consacre une partie de son activité physiologique à l'élaboration de son squelette. La connaissance de sa morphologie et de sa physiologie est donc une étape préliminaire indispensable pour comprendre les mécanismes de formation de celui-ci. L’entièreté du processus de biominéralisation ne dépend pas simplement de principes fondamentaux issus de la minéralogie inorganique mais aussi de mécanismes cellulaires particuliers. La caractérisation minéralogique d'un squelette devrait donc être systématiquement liée à une étude histologique et cytologique des cellules impliquées dans la formation du biominéral. La thèse présentée ici a suivi une telle approche multidisciplinaire de certains mécanismes de biominéralisation du squelette basal de plusieurs éponges hypercalcifiées actuelles, considérées comme reliques d'espèces plus anciennes du Paléozoïque et Mésozoïque.<p>Les trois premiers chapitres de cette thèse concernent l'espèce calcaire de Méditerranée, Petrobiona massiliana, une éponge hypercalcifiée actuelle plus accessible que d'autres principalement distribuées dans les mers tropicales. Une approche de sa morphologie générale a été réalisée en préliminaire à une étude de ses mécanismes de biominéralisation, intégrant une caractérisation minéralogique et biologique. Le quatrième chapitre compare d’un point de vue minéralogique le squelette basal de huit autres espèces hypercalcifiées tropicales appartenant aux démosponges.<p>Au cours du premier chapitre, d'importantes modifications morphogénétiques à l'échelle tissulaire et cellulaire, liées à certaines phases du cycle biologique et aux conditions environnementales, ont ainsi été mises en évidence chez Petrobiona massiliana. Par l'observation de modifications de l'organisation et de l'ultrastructure des cellules de réserves remplissant les cordons trabéculaires, structures spécifiques de l'espèce, un rôle dans l'approvisionnement nutritif des cellules de l'éponge ainsi qu'un caractère toti- ou pluripotent leur ont été conférés. Les fonctions potentielles de ces cellules dites de réserves pourraient permettre à l'éponge de maintenir des activités physiologiques importantes, telles que la calcification, au cours de son cycle vital. Finalement, l'analyse ultrastructurale des tissus de P. massiliana a permis d'identifier les basopinacocytes, cellules délimitant les tissus mous du squelette basal, comme le type cellulaire ayant le plus de probabilité d'être impliqué dans la formation de ce dernier.<p>Dans le deuxième chapitre, des granules de 50 à 100 nm de diamètre se sont avérés les plus petites unités structurales du squelette basal de Petrobiona massiliana, probablement déposées initialement dans un état amorphe à consistance molle. Des observations en MEB et MET ont mis en évidence l'assemblage de ces granules en amas ou fibres, ces dernières étant elles-mêmes latéralement associées en faisceaux. Un modèle impliquant la propagation de la<p>cristallisation au travers de ces assemblages de granules submicroniques a été établi pour expliquer le caractère monocristallin des unités microstructurales, démontré par diffraction électronique en MET. Leur assemblage en une microstructure particulière produisant des couches\ / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

With respect to the principles of biomineralization, it is of interest to study the crystallization of calcium oxalates under various experimental conditions. Calcium oxalates play decisive roles as biominerals in plants and as pathological “urinary/kidney stones” in vertebrates. Calcium oxalate exists in three different hydration states; calcium oxalate monohydrate (COM, monoclinic, a = 6.290(1)Å, b = 14.583(1)Å, c = 10.116(1)Å, β = 109.46°, P21/c), calcium oxalate dihydrate (COD, tetragonal, a = b = 12.371(3)Å, c = 7.357(2)Å, α = β = γ = 90°, I4/m) and calcium oxalate trihydrate (COT, triclinic, a = 6.11(1)Å, b = 7.167(2)Å, c = 8.457(2)Å, α = 76.5(2)°, β = 70.35(2)°, γ = 70.62(2)°, P ). Monoclinic COM and tetragonal COD are the most common phyto-crystals and the main constituents of kidney and urinary stones. The occurrence of calcium oxalates in plants represents a useful biogenesis (protection against herbivores) unlike the devastating occurrence in renal tubules. Therefore, biomineralization can be physiological or pathological. A systematic investigation of the morphological evolution of calcium oxalates in the presence of organic components is essential for understanding the mechanism of “pathological biomineralization”. In order to understand the pathological biomineralization of uroliths, it is necessary grow calcium oxalates comparable in morphology under similar growth conditions. The formation of calcium oxalate stones within a gelatinous state of proteins, polysaccharides, lipids and other biomacromolecules under a flow of supersaturated urine supports the fact that an “organic” gel model can simulate the process of urinary stone formation under in vitro conditions. Furthermore, synthetic polymers with precisely known functions and solution behaviours are better choices to understand the interaction of acidic proteins with calcium oxalates. Therefore, as a first step to unravel the complex pathology of uro/nephro lithiasis, we started to examine the structure and morphology of calcium oxalates crystallized in the presence of organic additives such as the sodium salt of polyacrylic acid (PAA) as well as agar gel. The influence of initial calcium oxalate concentration, pH and concentration of the additives on the formation of hydration states of calcium oxalates have been investigated along with the stated general methods. Apart from the three hydrated forms, calcium oxalate exists also in the anhydrous form (COA). Although three modifications of COA (α, β and γ) are reported in the literatures, the crystal structures and phase transformations were controversially discussed. We have been able to reveal the crystal structure of the β-modification of the anhydrous calcium oxalate by a combination of atomistic simulations and Rietveld refinements on the basis of powder X-ray diffraction pattern. β-COA belongs to the monoclinic system with unit cell parameters, a = 6.1644(3)Å, b = 7.3623(2)Å, c = 9.5371(5)Å, β = 90.24(2)°, P2/m (No. 10). The dehydration of COM was mimicked in silico to receive an initial model of the crystal structure of anhydrous calcium oxalate. This general approach may also be accessible for other decomposition processes ending up with crystalline powders of unknown crystal structure. No evidence for transformations from or to the α- or γ- modifications was found during our investigations. The growth pattern of COD crystals precipitated from aqueous solutions in the presence of PAA is clearly dependent on the concentration of PAA. By increasing the concentration of PAA, the shape of COD has been found to change from tetragonal bi-pyramids with dominant (101) pyramidal faces to tetragonal prisms with dominant (100) prism faces and finally to dumbbells. At still higher PAA concentrations, the morphology is reverted back to rod-like tetragonal prisms. Apart from these experiments, the interaction of PAA with (100) and (101) crystal faces of COD was explored with the aid of atomistic simulations. The simulation confirmed that during the development of the aggregates, strong interactions of PAA with the (100) faces take over control of morphologies. Our investigations show that the inner architecture of all the morphological varieties of COD was found to be dominated by an inner “core” consisting of thin elongated crystallites together with incorporated PAA and an outer “shell” formed as a consequence of secondary nucleation processes. We propose that for all types of COD aggregates, relative proportion of calcium oxalate and PAA dictates the shape and formation of nanometer sized crystallites which then aggregate and align to form the core. Such cores enriched with PAA may act as the sites for secondary nucleation events of calcium oxalate crystallites which then cover the core like a shell. In vitro experimental models for the growth of calcium oxalates can give valuable information on the growth and aggregation of urinary stones. Therefore, the “double diffusion technique” in agar gel matrix has been used for the biomimetic growth of calcium oxalate (COM) stones. A great variety of morphological forms of COM are produced in agar gel matrices (2 wt.-% agar gel of pH 8.5) ranging from platy crystallites to dumbbells and spherulites. The COM dumbbells and spherulites are assumed to be formed by the aggregation of smaller crystallites as a consequence of increased supersaturation inside the gel. Moreover, an increase of the pH value of the agar gel has been found to suppress the growth of COM and favours the growth of COD. The morphology of COD crystals grown in 2 wt.-% agar gel of pH 11.5 includes tetragonal prisms and dumbbells. The system calcium oxalate/ PAA/ H2O is a suitable model system for the investigation of principles of biomineral growth (shape development) in general. Our results demonstrate that the double diffusion technique in agar gel is a convenient route to grow calcium oxalate aggregates showing close resemblance to biogenic calculi and to study their ontogeny.